Ecosyste.ms: Issues

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GitHub / Bioconductor/SummarizedExperiment issues and pull requests

#79 - Clarify withDimnames=FALSE in the documentation

Issue - State: closed - Opened by SamGG 9 months ago - 3 comments

#78 - add a section about interactive visualization

Pull Request - State: closed - Opened by kevinrue 12 months ago - 1 comment

#76 - Depreciated function calls in DelayedArray

Issue - State: closed - Opened by mingl1997 about 1 year ago - 4 comments

#75 - Warning and error message when using '$' operator on summarizedExperiment object

Issue - State: closed - Opened by DijkJel over 1 year ago - 5 comments

#73 - colData Default in Constructor Inconsistency

Issue - State: open - Opened by DarioS over 1 year ago - 1 comment

#72 - metadata function is not exported as others

Issue - State: closed - Opened by hsiaoyi0504 over 1 year ago - 1 comment

#70 - Curious about how Rd manuals are generated

Issue - State: closed - Opened by mvfki over 1 year ago - 3 comments

#69 - Add an `assaybind()` method

Issue - State: open - Opened by multimeric over 1 year ago

#67 - Erroneous behaviour when colData is data.frame

Issue - State: open - Opened by TuomasBorman almost 2 years ago

#66 - `combineCols` should keep names in metadata with `use.names=TRUE`

Issue - State: open - Opened by LTLA almost 2 years ago

#65 - Remove all dimnames in `combine_assays_by` to avoid constructor check failures

Issue - State: closed - Opened by LTLA about 2 years ago - 3 comments

#64 - `all.equal(x, y)` vs `all(x == y)`

Issue - State: closed - Opened by LiNk-NY over 2 years ago - 3 comments

#63 - Constructor could check that assay is in matric format

Issue - State: closed - Opened by TuomasBorman over 2 years ago - 2 comments

#62 - Consider assayData DataFrame for assays

Issue - State: closed - Opened by jmw86069 over 2 years ago - 6 comments

#61 - `combineCols()` and `combineRows()` not listed in 'Usage' section

Issue - State: closed - Opened by PeteHaitch over 2 years ago - 4 comments

#60 - Enforce unique assay names

Issue - State: open - Opened by hpages over 2 years ago - 2 comments

#59 - Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()?

Issue - State: open - Opened by hpages almost 3 years ago - 1 comment
Labels: enhancement

#58 - subset fails when subsetting a SummarizedExperiment object with no samples

Issue - State: closed - Opened by kpagacz about 3 years ago - 11 comments

#57 - Adding checkDimnames=FALSE to the SE constructor

Issue - State: closed - Opened by LTLA about 3 years ago - 1 comment

#56 - Constructor assigns wrong assay values to wrong samples and features

Issue - State: closed - Opened by TuomasBorman about 3 years ago - 7 comments

#55 - Subsetting

Issue - State: closed - Opened by antagomir about 3 years ago - 2 comments

#54 - add dims note

Pull Request - State: closed - Opened by LiNk-NY about 3 years ago - 1 comment

#53 - Add rownames check for cbind()

Issue - State: open - Opened by tavareshugo about 3 years ago

#52 - Vignette Doesn't Specify Dimensionality Rules

Issue - State: closed - Opened by DarioS about 3 years ago - 1 comment

#51 - assay<- is too pedantic when the dimensions are named

Issue - State: closed - Opened by LTLA about 3 years ago - 2 comments

#50 - Add a showAsCell method for SummarizedExperiment objects

Issue - State: closed - Opened by LTLA over 3 years ago - 1 comment

#49 - Conversion to SingleCellExpriment object

Issue - State: closed - Opened by zhli12 over 3 years ago - 1 comment

#48 - Migrate SCE's flexible row combiner for general SE use.

Pull Request - State: closed - Opened by LTLA over 3 years ago - 10 comments

#47 - fail to create `rbind` for SE-derived class due to the validity check

Issue - State: closed - Opened by fionarhuang over 3 years ago - 2 comments

#46 - More informative error message for mismatching numbers of rows

Issue - State: open - Opened by LTLA almost 4 years ago

#45 - Add utility to easily split rows/columns by a factor.

Pull Request - State: closed - Opened by LTLA almost 4 years ago - 1 comment

#44 - loading package taking too much memory

Issue - State: open - Opened by spocks about 4 years ago - 2 comments

#43 - Coercion from SummarizedExperiment to ExpressionSet creates an unlocked environment

Issue - State: closed - Opened by tomsing1 about 4 years ago - 3 comments

#42 - “SimpleAssays” is not a defined class

Issue - State: closed - Opened by Georgy415 over 4 years ago - 2 comments

#41 - Incorrect document page

Issue - State: closed - Opened by Jiefei-Wang over 4 years ago - 2 comments

#39 - Type conversion btw SimpleAssays and list

Pull Request - State: closed - Opened by Jiefei-Wang over 4 years ago - 2 comments

#37 - error object 'normalize_names_replacement_value' not found

Issue - State: closed - Opened by weibei43 over 4 years ago - 9 comments

#36 - colData assignment should fail but does not

Issue - State: open - Opened by vjcitn over 4 years ago - 1 comment

#35 - colnames-related concerns

Issue - State: closed - Opened by vjcitn over 4 years ago - 5 comments

#34 - Resolve _R_CHECK_LENGTH_1_LOGIC2_ issue

Pull Request - State: closed - Opened by LiNk-NY almost 5 years ago - 2 comments

#33 - Slightly relaxing the rowData checks for cbind

Issue - State: open - Opened by LTLA almost 5 years ago

#32 - Build an assay element to work from my own normalized count matrix

Issue - State: closed - Opened by ramarquezo about 5 years ago - 5 comments

#31 - Extraction isn't working with ShallowSimpleListAssays on Bioc Devel 3.10

Issue - State: closed - Opened by mjsteinbaugh about 5 years ago - 4 comments

#30 - Should `rowData` be merged with `mcols(gr)`?

Issue - State: open - Opened by LiNk-NY about 5 years ago - 2 comments
Labels: question

#29 - derived RSE to SE coercion discards names

Issue - State: open - Opened by LTLA about 5 years ago - 15 comments

#28 - seqinfo<-() fails when @rowData is a GRangesList

Issue - State: closed - Opened by lawremi about 5 years ago - 2 comments

#27 - c() does not work on SummarizedExperiment

Issue - State: open - Opened by lawremi about 5 years ago - 1 comment

#26 - SummarizedExperiment R package not allowing installation.

Issue - State: closed - Opened by joao1980 about 5 years ago - 8 comments

#25 - assayNames<- is reluctant to work

Issue - State: closed - Opened by LTLA over 5 years ago - 5 comments

#24 - Why is SummarizedExperiment graphic not directly included in package?

Issue - State: closed - Opened by PeteHaitch over 5 years ago - 4 comments

#23 - SummarizedExperiment::cbind

Issue - State: open - Opened by tiagochst over 5 years ago - 3 comments

#20 - Convert ShallowSimpleListAssays into an S3 list

Issue - State: closed - Opened by marcpaga over 5 years ago - 3 comments

#19 - Allow clearing of colData

Issue - State: closed - Opened by LTLA almost 6 years ago - 1 comment

#18 - Added SE coercion advice to derivation vignette

Pull Request - State: closed - Opened by LTLA almost 6 years ago - 1 comment

#17 - SummarizedExperiment doesn't work with data.frame input

Issue - State: closed - Opened by LTLA almost 6 years ago - 4 comments

#16 - all.equal does not work for SE objects

Issue - State: closed - Opened by LTLA almost 6 years ago - 5 comments

#15 - Advised on implementation of SE coercion methods

Pull Request - State: closed - Opened by LTLA almost 6 years ago - 1 comment

#14 - Error in coercion SummarizedExperiment <-> ExpressionSet

Issue - State: closed - Opened by lgeistlinger about 6 years ago - 1 comment

#13 - rowData rownames issue explored at BioC2018

Issue - State: open - Opened by mikelove about 6 years ago - 6 comments

#12 - Use DelayedArray:::set_dimnames() in realize,SummarizedExperiment-method

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 2 comments

#11 - Fix 'getter' example in 'Extensions' vignette

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#10 - Detailed instructions for class extension

Pull Request - State: closed - Opened by LTLA over 6 years ago - 23 comments

#9 - Add BACKEND argument to realize,SummarizedExperiment-method

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago

#7 - Difficult bug when colnames are arrays

Issue - State: closed - Opened by LTLA over 6 years ago - 6 comments

#6 - addition of explicit subset method for SummarizedExperiment class

Pull Request - State: closed - Opened by schifferl over 6 years ago

#5 - import / export as loom

Issue - State: closed - Opened by mtmorgan over 6 years ago - 1 comment

#4 - Fix broken link to SummarizedExperiment doc

Pull Request - State: closed - Opened by LiNk-NY over 6 years ago

#3 - HDF5ArraySeed slot name 'filepath' instead of 'file'.

Pull Request - State: closed - Opened by Liubuntu over 6 years ago - 1 comment

#2 - rowData does not contain the rownames

Issue - State: closed - Opened by LTLA almost 7 years ago - 34 comments

#1 - More informative errors for assay() with names.

Pull Request - State: closed - Opened by LTLA almost 7 years ago